Bulk RNA-seq ITK-SYK
RNA-seq
No filtering on count matrix for TPM calculation.
Filtering only on count matrix.
Filtering
Count matrix : This count matrix was modified like followings.
B cell genes out (Cd79a, Cd79b, Jchain)
Immunoglobulin genes out
“Ighv* ,”Igl* , “Igk*
Genes like”Igf* , “Igl* (Starting with Ig- but not Immunoglobulin
genes) are not removed (checked manually)
TPM table (downloadable)
PCA
PCA plot
PCA plot by condition
DEG analysis
DEG 1B vs S
DEG information table
Volcanoplot
DEG 2B vs S
DEG information table
Volcanoplot
DEG 2B vs 1B
DEG information table
Volcanoplot
ssGSEA
Single sample GSEA
Single-sample Gene Set Enrichment Analysis (ssGSEA) is an variation
of the GSEA algorithm that instead of calculating enrichment scores for
groups of samples (i.e Control vs Disease) and sets of genes (i.e
pathways), it provides a score for each each sample and gene set
pair.
(https://www.genepattern.org/modules/docs/ssGSEAProjection/4#gsc.tab=0)
ssGSEA heatmap
Color represents enrichment score
Significance by p value Heatmap
Red: p value <= 0.05 (significant)
White : p value > 0.05 (not significant)
Next work
To be discussed.